Pokemon Legacy
by Red Eyes Black Dragon Master
Summary: Years have past. Ash is now 18 and ready to come home. But not all is well. Someone has been murdering the gym leaders and destroying the Pokemon centers. Who is causing this? Can Ash manage to save his home, or will it all come crashing down around him?
1. A Hero Comes Home

**Pokemon Legacy**

**A Hero Comes Home****  
**

Late at night, Erika stood in the Celadon City Gym watering her plants just before she was to go to sleep. Her Gloom walked up beside her and nuzzled her lightly. "Gloom, gloom gloom." It said. Erika placed her hand on her Pokemon's head, stroking it.

"I know, I'm going. You don't have to worry." Erika said. She placed the water pail down and knelt down, embracing Gloom in her arms. She glanced out the window at the starry night sky. Was tonight the night? She'd heard about what had happened to many of the others. "Okay, Gloom. Let's go." She stood up and started towards the door. As she passed the window, she caught sight of something fly across the sky. She stopped to get a better look, but by then it was gone.

Erika stared hesitantly out her window. Holding one hand over her torso and the other by her mouth, she couldn't help but look down in concern. "Gloom, hurry we have to go now!"

A sudden spark of electricity exploded from outside and the lights inside the gym shorted, turning the entire building dark. A loud bang came from the door. Erika stopped in her tracks, her breathing became fast, cold sweat pricked on her forehead. It was too late, now. The door buckled inward with another loud bang. With a third bang, the door came off it's hinges and clanged to the ground. A large orange Charizard stepped inside, swinging it's tail back and forth, the flame at the end blazed brightly. It roared and snarled.

Erika tried to run, but tripped and fell to the ground. Charizard waked in, holding it's wings high above it's head. Gloom jumped in between Erika and the huge fire pokemon. "Gloom, Poison Powder!" Erika shouted. Instantly, purple powder secreted from the plant pokemon's head and filled the air, drifting towards the fire dragon.

"Gust, Charizard." A clam voice said from outside. Charizard flapped his wings, blowing the poison dust back towards Glom and Erika. "Flamethrower." A powerful blast of flames erupted from the Charizard's mouth. The gym caught fire, the orange and red flames spread across every tree and plant in the room, filling the room with smoke.

"NO!" Erika gasped and coughed in the smoke filled room. Gloom grabbed her and started to pull, trying to save it's trainer. Suddenly, Gloom was torn away. Erika watched in horror as Charizard lifted the struggling Grass Pokemon in it's jaws and crunched. The fire dragon shook Gloom violently back and forth. "Stop! Please! Don't do this!"

Charizard dropped the mortally wounded Gloom to the ground and walked away, moving back towards the door. It turned around just as it walked out and shot another blast of flames around the door frame, trapping Erika and Gloom. Erika grabbed hold of her dying Pokemon and held it in her arms. She wept as the gym burned around her.

**/**

Professor Oak placed down the days newspaper. Another murder, Erika's Gym this time. He placed his hands across his eyes in sadness. In the past few months, gyms all across Kanto have been destroyed and the Gym leaders murdered. First it was the Viridian Gym. Gone ago up in flames five months ago. At first it was thought to be just a random and unfortunate event, but then only three weeks later the Saffron City Gym, as well as the Pokemon center in that town, were both destroyed in the same night. Many people died, including Sabrina.

Since then, many of the gyms in Kanto had been destroyed, all during the night. Cinnabar Island, Vermillion City, Fuchsia City, and now Celadon city gyms had each been destroyed. Trainers all over the region had become terrified, the entire police force of officer Jenny's was mobile all over Kanto. Along with the gyms, the Pokemon centers and the police stations had also been destroyed, resulting in many more dead.

Oak sighed. He ran his fingers over his forehead. He felt hopeless, unable to really do anything about the situation aside from stand here in his office and read from the papers about how the next gym leader would die.

The video phone in the corner began to beep, the red light next to the screen flashed on and off. Professor Oak stepped to it and picked up the head set. The screen flashed and Ash Ketchem's face appeared on the screen.

Now in his late teens, Ash had now grown to almost six feet tall. He wore a version of his old outfit, his sleeves torn off at the shoulders. His hair now longer almost to the base of his neck, and dark stubble grew along the sides of his face and chin. Held in Ash's now strong arms, was Pikachu. The small electric mouse's tail hung limp over the side of Ash's arm. "Hi, Professor Oak." Ash's voice scratched over the speaker.

"Ah," A smile came over Oak's face upon seeing his most successful protégée. "Ash, how is everything going out there? Is Pikachu okay? Ever since that accident with Paul, I've been worried."

"Yeah, Pikachu's fine."

As if to comment itself, Pikachu pushed itself up on its front legs and squeaked. "Pika!"

"Well, that's good. Has Paul given you any problems since then?" Oak asked.

"No, I've decided to let it go. He doesn't bother me anymore."

"Always good to hear." Oak said. "What are you up to now?"

"Actually, I was thinking of coming back to Kanto for a while." Ask said. "You know, to visit you, Mom, Misty, and Brock."

Professor Oak shook his head slightly from side to side. "Are you sure you want to come back now? Things have been rather upsetting around here this past while."

Ash nodded and glanced to the ground. "Yeah, I heard. I was so distraught when I heard about what was going on. That's actually why I decided to come back. I what to make sure Misty and Brock are still okay."

"Yeah, they're still okay, for now anyways." Oak said. "Although if you are coming back, I hope you get here fast. Where are you now?"

"East Johto. I should be there by tomorrow. See you soon, Professor. Tell Mom I said 'Hi.'" The screen turned black as Ash hung up the phone. Oak placed his head set down as well. A smile had slowly crept over his face. At least Ash was still doing okay after everything that had happened.

/

Misty strolled down towards the Pewter City Gym, her feet felt aching after the walk from Cerulean. It had been a long time since she walked so far in a day. She pushed the doors open and walked inside. "Brock?" her voice echoed in the darkness.

"Misty." Brock got up from the far end of the gym and walked over. His arms held out to his sides, taking Misty in a strong embrace. "It is so good to see you, you never come by anymore."

"Ack!" Misty squirmed to get out. She gasped for breath as Brock set her down. "Nice to see you, too." She dusted herself off. She let her hair flow down now, no longer tied up to the side. Wearing shorts that came to her knees and a low cut shirt that exposed her navel, and a long coat which came down to her ankles, she now had the appearance of a strong, independent, young woman. "I came by to make sure you were still okay."

"Nothing yet. But that can't be the only reason you're here. If that was all, you would've just called." Brock folded his arms. "Why are you really here?"

"Fine." Misty scoffed. "I got a call earlier today from Professor Oak. He said Ash was on his way back."

"Oh, really? Wow, I can't believe it. He hasn't been back home for over two years. I mean, a trip to the Orre Region is no simple task." Brock said. "Have you decided to tell him yet?"

Misty turned away slightly, she held her arms around her midsection and looked longingly at the ground. "I…I still can't decide if I should. What will he say? How will he react? To know that…I…"

"You really need to tell him the truth." Brock placed his hand on her shoulder. "He's going to find out one way or another. Would you prefer if I do it?"

"No!" Misty grabbed Brock's hand tightly. "No, I need to tell him personally."

"Hopefully you do. It would probably bring up his spirit's a little, especially after what happened to Pikachu." Brock said.

"I wasn't there when it happened, what happened to Pikachu?" Misty asked.

Brock sighed. He sat down on a rock and ran his fingers through his hair. "Paul. Paul happened." He said.

"What do you mean?" Misty asked.

"After the Sinnoh championships, Paul challenged Ash to another battle, Pikachu against his Electabuzz. For a while the battle was pretty even, but then Ash tried to a Volt Tackle. As Pikachu tried to charge Electabuzz, Electabuzz grabbed him and used a Thunder Punch right on Pikachu's back. We took Pikachu to the Pokemon center but, it was no use. Pikachu's spine was severed. He's paraplegic now, can't use any of his speed or agility based attacks."

The door to the gym clicked open again and a beam of light fell in from the door. Nurse Joy, in her off duty clothes of long jeans and a long sleeve shirt, stepped inside holding the hand of a small child. The child, a four-year old boy with his thumb in his mouth, looked up at Brock and squealed. "Daddy!" The child ran full bore towards Brock, arms out stretched.

"Hey, it's my little man!" Brock crouched down and caught the little kid in his arms, lifting him up and spinning him around. The kid squealed and squirmed in Brock's arms. "How was school today for you, Nathan?"

"He did very well today, Brock." Nurse Joy said. "He's starting to learn his simple addition and subtraction."

"Really, that's pretty good." Holding Nathan in one arm, Brock scooped up Joy in his other arm and pulled her close, planting his lips against hers. Joy kissed him back, placing her hands on his face. "I've missed you." He said as he pulled back.

"I know." She smiled.

Misty stood up and walked over to the small family. "This your little boy?" She asked.

"Yup, the joy of my life." Brock said.


	2. Gary's Message

**Gary's Message**

High over the sky of Cerulean, a great winged creature soared. It's mighty black shape body made it nearly invisible in the night, only the disappearance and reappearance of stars gave it away. It's long swan-like neck leading the way and a long powerful tail trailing behind it. On it's back, a single trainer watched as the city zoomed by beneath him.

They came to a large building with a plaster Dewgong adorning the entrance. The Cerulean Gym. The giant Pokemon stopped and hovered over the gym. It craned it's head back and looked at the trainer. The trainer pointed one finger down at the gym and nodded, quietly.

The powerful Pokemon turned back and opened its mouth. A ball of gold energy began to form, and then a beam of pure energy shot down and struck the gym. It exploded, orange and yellow flames reached out from the sides and top along with black smoke. Shrapnel and debris flew from the burning rubble of the gym.

The great Pokemon flapped its enormous wings and continued flying west.

As it left, a ways in the distance another Pokemon watched. One with a humanoid shape and a long thick tail. It stood on the side of a mountain, resting its three fingered hand on the rock as it watched the giant bird like Pokemon disappeared to the horizon. _"I sense the presence of that mind. That human's mind. A presence I haven't felt in a long time. But, why?"_

/

Gary Oak, young and talented Pokemon researcher, sat at his computer table typing away furiously. The documents opened and closed on the screen. Like many people, he was interesting in the recent killings of the Gym Leaders as well as the attacks on the Pokemon Centers and Police Stations.

He was rapidly compiling as much of the evidence together as he could. True, he wasn't officially on the part of an investigation team, but he was trying to put things together. All the gyms had their power shut off by a power surge, probably caused by an electric Pokemon. Alone that wouldn't do much to change the case, but some new information regarding the recent destruction of Erika's gym could help.

Reports say it was a Charizard that was attacking. The National Pokemon Institution had a composed list of all the Pokemon owned by all registered trainers. By complying all the Pokemon that were used in the attacks Gary should be able to make a short list of possible trainers and suspects.

As Gary thought about it, he became more sure of the idea that it wouldn't even be a registered trainer. It could easily be Team Rocket, or some other terrorist organization. Could Giovanni be behind it? The Viridian Gym was the first one destroyed, it would make sense that Giovanni would want to get rid of the one that used to be owned by his organization. Maybe Team Rocket was trying to make some kind of massive plan? But if that was the case, then why did they attack the gyms sporadically and not all at once?

The computer had finished processing and a list of names appeared on the screen. Some of the Pokemon used during the attacks were a Infernape, Charizard, and a Tyranitar. Of all the trainers registered in the Official Pokemon League, only fifteen trainers had all three. Gary proceeded to cross check all the trainers to find if any of them had a powerful electric Pokemon, one strong enough to short out the power to an entire Gym. Or if any of their Pokemon knew an electric attack

The numbers dwindled to five. Gary leaned back in his chair and scratched his chin. All five of the trainers happened to be in other regions. Two in Hoenn and the other three in Johto. Which obviously meant that whoever was causing the attacks was not registered in the system.

He leaned back and ran his fingers through his hair. He sighed. The law enforcement had probably already tried this once before anyways, so what was the point? Looking at all the names of the trainers on the computer screen gave Gary a feeling of nostalgia. It had been a long time since he was a trainer. All those years traveling and capturing as many Pokemon as he could. Well over 400 in his collection at one point. But now, he only had one. Blastoise, his first Pokemon. His hand fell to the single poke-ball on his belt.

Thinking about his life as a trainer brought back specific memories of his old friend. Ash. Gary remembered all making sure to outdo him in every way, catching more Pokemon and more of each one to make sure that he had more than Ash. There must've been a downside to that considering he lost to Ash in the Johto finals. Maybe it was since Ash kept the same ones all the time those few were especially strong.

As he thought more about it, a thought crept into his head. Where was Ash now? How many Pokemon had he caught at this point? Quickly, Gray punched Ash's name in the database and watched as the computer did its thing. What kind of creatures did he have these days? Gary stared sternly as the computer brought up a single phrase.

No Entry.

He tapped his finger against the desk. That was strange, Ash's trainer data was gone, like it had never been there. But that was impossible.

At that second, the ground started to rumble. Gary shot up from his chair and backed away from the computer, glancing all around the room as the rumbling grew closer. He grabbed the poke-ball from his belt and pressed the button on the front, growing it to full size. The wall to his left exploded into ruble and splinters as a large dark green reptile like creature over seven feet tall smashed through the wall. A Tyranitar.

Gary threw his poke-ball in the air and in a blast of light, his Blastoise appeared. The large blue two-legged turtle roared and cocked it's guns. "Hydro Pump!" Gary pointed at the Tyranitar. Two powerful streams of water shot from the cannons on Blastoise's back and slammed into the large dinosaur like Pokemon. It was thrown back and crashed through the far wall.

Tyranitar pushed itself back up and knocked the rubble away. It tried to advance, but staggered, severely weakened by the water. It growled and shook its head, shaking the water away.

"Hyper beam." A calm voice said. Tyranitar reared back and blasted a powerful beam of gold energy from its mouth, aimed right at Gary.

As the energy came barreling towards Gary, Blastoise jumped between Gary andf the Hyper Beam, taking the full blunt of the blast. The giant tortoise growled in pain, but it held its ground. The energy finally dissipated. Fortunately, its shell managed to absorb most of the damage. It turned to face its opponent, glaring.

"You okay, big guy?" Gary placed his hand on his Pokemon's shell. Blastoise nodded. "Good. Skull Bash!" Blastoise charged and rammed Tyranitar headfirst. The two Pokemon crashed to the ground, Tyranitar gasping for breath.

As Blastoise got back up, a red beam of light struck Tyranitar and it disappeared inside it's poke-ball. Its trainer stepped inside the destroyed building and his eyes met Gary's. Gary stared in shock and horror. "No, that's impossible. It's been you all along?"

"The one and only. You are part of the problem. And need to be extinguished." The trainer took another poke-ball from his belt and it expanded. A burst of white light exploded from that ball and a near pure-white Pokemon almost 20 feet tall appeared. It spread its huge wings and craned back its long neck. It sang a deep and powerful song that echoed thought the night.

Gary fell back at the sight of the manificent creature. A true legend, the Guardian of the Sea. Gary took his poke-ball and recalled Blastoise. He ran to his computer and activated the Pokemon transportation system. His fingers moved wildly across the keyboard, typing as fast as he could. A few more seconds. "Gary, is that you?"

/

In his lab, Professor Oak sat at his table. Coffee in one hand, research documents in the other. Just then the light at the computer started to flash. He placed the papers down and turned the screen on, his grandson appearing in the screen, frantically breathing heavily and typing away. "Gary, is that you?"

"Gramps," Gray placed his Poke-ball on the teleporting pad, "turn your transporter on! I'm sending you Blastoise!"

"Gary, what's going on over there?" Oak asked. His transporter hummed and the Poke-ball appeared in a flash of white light.

"He's here, the person who's been attacking the Gym's and Pokemon Centers. I know who it is. It's-" The screen cut out and static flashed crackled.

Professor Oak stared at the black and white static where is grandson used to be, in total shock. The Gym Leader killer was there? Why was his there? Oh, no. Oak jammed his fingers against the keys as fast as he could, trying to get the image back, but nothing worked. Gary was gone…

Oak slumped down into his chair, his hands wringing though his hair, tears falling to the keyboard. His grandson, who held such promise and who he loved, had become another casualty of this crisis.


	3. The War of Unova

**The War of Unova**

A knock rang against the door. Delia Ketchum dried her hands on a nearby towel and came out of the kitchen. She opened the door, and standing there was Brock, Misty, Joy, and little Nathan. "Misty, Brock, it's good to see you again."

"Hello, Mrs. Ketchum." Misty waved. "How are you doing?"

"I'm doing just fine. Did you come by to see the little guy? He's sleeping right now." Delia held the door open as the small group stepped inside. While Brock, Joy, and Nathan sat on the couch in the living room, Misty made her way to Ash's former room at the far end of the house.

Misty turned the handle and slowly pushed the door open. She peaked inside and saw a white baby crib. A small scruff of black hair covered the top of his head and his eyes closed in sleep. A smile crept across her face as she stepped inside and closed the door behind her. She rested her arms on the side of the crib, gazing down at the sleeping baby.

He was so adorable, the most beautiful thing she had ever seen. She ran her finger lightly over his face. He twitched slightly, before seeping back to sleep. The time past without her noticing. As she watched, the baby squirmed and began to wake. He started to cry. "Oh, Adam, are you hungry?" Misty picked him up and cradled him in her arms. She carried him over to a chair in the corner and began to feed him.

/

Back in the living room, Brock and Delia engaged in small talk. "Have you heard from Ash lately?" Brock asked. "He contacted Professor Oak, Misty and me the other day. Where is the Professor? Still in his lab?"

Delia averted her eyes, fixing them on the floor. "I don't suppose you heard. Last night, Gary was attacked."

"Attacked?" Brock inched forward. "By who?"

"The person who's been attacking the gyms. They came after him. All me managed to do was send is Blastoise back to Oak before the connection cut out." Delia said. Slowly, she wiped a tear from her eye.

Brock folded his hands and stared grimly at the carpet. After a moment of silence, he grabbed the remote off the coffee table and flipped on the TV. Instantly the image of a reporter standing in front of a smoldering pile of rubble appeared. "Last night at around 2:00 AM the Cerulean Gym was destroyed. We have no idea how this incident occurred, but several eyewitnesses have stated that a beam of energy struck the gym from the sky."

Brock quickly shut the TV off. He sighed, his hand reached to his shoulder, rubbing an old injury. "Is it aching again?" Joy asked, Nathan settled on her lap.

"A little bit. The shot of the gym just brought back some memories of Unova." Brock said. The War of Unova had been over for three years but even so some of the images Brock had seen over there still burned in his mind. Every able bodied Pokemon trainer from across the Kanto Region had been sent to Unova to fight.

Ash and Brock had been assigned the same platoon, as a Gym Leader Brock was automatically assigned the rank of Sergeant and commander over the newly recruited Privates, including Ash. After the basic training, Brock lead his ranks in the Battle of the Bridge. The bridge to the Elite Four of the Unova region. A fight that was supposed to only last a few days dragged on for over a month.

Pokemon against pokemon, trainer against trainer, the river turned red with the blood of all those who died. Brock was pushing forward with his Steelix, but the resistance was too great. A Hydreigon had snuck up to him. Brock saw the pokemon too late, as it's huge jaws came towards him, sharp teeth preparing to tear away flesh. Brock tried to move, but he was caught. The powerful jaws clamped over his shoulder, digging into his skin. His bones began to crack under the pressure. He screamed in agony but the pokemon would not release it's hold.

That is until the Hydreigon was struck by a Charizard. The black and gray pokemon was propelled through the air, crashing back to the ground in a bone shattering thud. Brock collapsed, holding the wound in his shoulder.

"Charizard, Flame Thrower!" A powerful blast of flames shot from the dragon-like pokemon's mouth, engulfing the Hydreigon. Brock felt someone grab his arm and start to lift him up. Ash pulled Brock's arm over his shoulders and began to carry him off the battle field. Behind them, Charizard continued to fight the Hydreigon.

At the medic tent, Brock rested on a stretcher. Attendants held wet rags over his injured shoulder, slowing the bleeding. He stayed there for the next five days. After which Brock was discharged from the war and sent home.

Even as Brock sat here on the couch at Delia's house, he still felt those days on the battle field. The cries of death and pain from the trainers on both sides as the pokemon killed each other. To this day he still had nightmares of the Hydreigon.

/

A hospital in Vermilion city. The Nurse Joy of that city walked inside and stepped to the front counter. The receptionist looked up and waved. "Hello, Joy. What brings you here?"

Joy smiled. "I'm here to see Dr. Farix for my appointment."

"Of coarse, he's waiting for you. Right down the hall. Third door on the left." The receptionist pointed to a series of doors to her left. Joy thanked her and walked towards the door.

She knocked lightly and a voice from inside told her to come in. She did and sat down on the waiting chair of the office. Butterflies fluttered in her stomach. Her first child, she couldn't believe it. She and her husband had been trying for so long and now they finally had some success.

Dr. Farix sat up from his desk. "Good to see you, Joy. Here for you're prenatal check up, I see. Come with me to the examination room and we'll get started." He led Joy out of the office and to the examination room. Joy relaxed on the examination chair and lifted her shirt above her naval. Dr. Ferix had the sonogram on and moved it over her stomach. He studied the images on the screen and a concerned look came over his face.

"What is it doctor?" Joy asked, taking notice of his stern look.

"I see something bad is happening. I'm going to have to look into it right away. If I'm right, the life of your child is in terrible peril."

"What!" Joy exclaimed. "What's wrong?"

"I don't know, but I'm going to have to go in and check first hand. I need to prep you for surgery right away."

Minutes later, Nurse Joy lay on the operating table. She looked worriedly back and forth as the doctors and surgeons moved about, prepping their equipment. She didn't know what to expect, but she was afraid. He first child and already it was in danger. Even the doctors didn't know what, but she put her full faith in their hands.

Dr. Ferix looked down over her. "Are you ready?"

She nodded.

"Good." He brought over the gas tube and placed it over her mouth. "This will cause you to fall asleep for the remainder of the process. When you wake up, it should be over." With a twist of the knob on the gas tank, a small hiss came through the tube and Joy's eyelids began to fall.

Once she was fully asleep, Dr. Ferix took the gas tank away. "Alright, we have just a few moments. He need to remove this embryo and implant a new one from the reserves. We have two hours. Let's move people."

It was standard procedure. If ever a Nurse Joy or Officer Jenny became pregnant, then when they came in for prenatal care the existing embryo was to be removed and then replaced by a fellow Nurse Joy or Officer Jenny embryo. A stockpile of cloned embryos where kept on stock within each of the major hospitals in the towns with pokemon centers and police stations. Dozens of future Nurse Joy's and Officer Jenny's. A potential army in the making. And complete control over the pokemon medical and law enforcement fields.


	4. The Truth Revealed

**The Truth Revealed**

Dr. Farix strolled down the street. Yellow beams shown down from the street lights, illuminating the darkness. At midnight, his shift had ended. So now he was on his way home. His hands held deep in his pockets and glasses settled lightly over the bridge of his nose. Under his left arm was a manila folder. The streets were empty and each of his footsteps echoed off the buildings.

As he came up to an alley, a shadowy figure stepped out and stood in his way. In the crook of his right arm he held a small pokemon. Dr. Farix jumped from the sudden appearance. "Whoa!" He pushed his glasses back into place. "Scared me there, kid. What are you doing out this late?"

"I know who you are," the shadow figure said. "A renowned doctor. The famous Dr. Farix, who has helped countless couples conceive and bare children. And also causing the deaths of hundreds of children."

"What?" Farix backed away, his heart beginning to race. Sweat peaked on his forehead. "What are you talking about, kid?"

"I know what you do. Government sponsored abortions, without the consent or knowledge of the parents." The figure stepped forward, reaching for a pokeball on his belt. "Human cloning on select patients, namely any Nurse Joy or Officer Jenny who would come in. Yes, I know what your doing."

Dr. Farix stumbled backwards, dropping the envelope and falling back to the ground. "How do you…who are you?"

"I'm upsetting your control. I'm bringing down the totalitarian control of the Pokemon League." He tossed a pokeball in the air and it burst open in a flash of light. A Charizard appeared, flapping its wings and swinging its flaming tail back and forth. Smoke rose from its nostrils as it eyed the doctor.

"You!" Dr. Farix shouted, point at the figure. "You're the Gym Killer!"

"Flame Thrower." He said in a cold emotionless tone.

Charizard took in a deep breath and unleashed a torrent of flames. Fire hot enough to melt boulders engulfed the doctor. He screamed in agonizing pain and his lungs fried in his chest when he tried to breath. As the screaming quieted down, Charizard stopped its fire. A black burnt corpse was all that remained of Dr. Farix.

The trainer walked up to the fallen envelope, untouched from Charizard's flames. He opened it and began to look though the pages. It was a warrant of arrest. Three pictures were given with it. Nurse Joy, Brock of Pewter City, and a young boy of about five or six. The trainer closed the envelope and climbed on the back of the Charizard, still holding the small Pokemon him his right arm. "Pallet Town." The Charizard shoved off against the ground and took off into the night sky.

Professor Oak slowly and delicately examined Blastiose. The back part of its shell had been scarred, as if hit by a powerful force, but nothing else was seriously wrong with it. He sprayed a Potion on it and steadily cleaned it's back with a medical rag. The spray stung the injury, and Blastiose groaned in pain.

"I'm sorry, old boy. Just need to work this through." He wiped the rag along the Pokemon's shell. Tears began to well up in Oak's eyes. This Pokemon was the only remnants of his grandson left to him. He wiped his tears away on his lab coat.

Blastoise turned to Oak. It groaned, tears also falling down its face. Oak looked up at the creature. This was the same Squirtle he had so long ago and had given to Gary on his first day as a trainer.

It held up a small letter in its hand. A final message from Gary. It handed the letter to Professor Oak, who took it with shaking fingers. Oak tore the top from the envelope and pulled out the folded slip of paper.

"Gramps, I have only a few seconds, so here it is. I love you and I'm sorry I can't say more. I know who the Gym killer is…"

Oak stared at the paper in stunned silence. The last few lines of the letter ran over and over in his mind. It was impossible, no way. But this was the message Gary had sent, his final words. But Oak couldn't believe it. It couldn't be him.

Two agents, dressed in all black, stood in the doorway of the home of Delia Ketchem. Only the bright stars of the night sky shown behind them. "We need to Talk to Nurse Joy and Brock, the Pewter City Gym leader." The one on the left said.

"What is this about?" Delia asked.

"It is a matter of national security. It is none of your concern." The first Agent said. He pushed past Delia and stepped into the house. "Brock, Joy, it's the Pokemon League Investigation Agency." The agent called out into the house.

From down the hall, Brock and Joy stepped into the room. Nathan tightly clutched Joy's hand. "Agents, what is it?"

The second agent stepped inside. He reached into his coat and pulled out a pair of handcuffs. The first agent also pulled a set of handcuffs from his coat. "You are both under arrest."

"What?" Joy grabbed her son and pulled him close to her. "What for?"

"Treason against the Pokemon League. Violation of your medical and Pokemon Gym Contracts." The agent grabbed Brock's arm and locked the handcuffs around his wrist. Pulling his other arm around his back, he restrained him.

"Hey! I never violated any of my contracts. What? Was it because I left the Gym in my dad's charge?" The agent remained silent. The second agent walked up to Joy and cuffed her as well.

"Momma!" Nathan shouted. He tried to cling to her, but the agent grabbed the child as well. Nathan screamed and kicked. The agent pulled a small syringe from his coat pocket and jabbed the needle in the child's neck. Nathan stopped kicking and fell limp almost instantly.

Misty came storming out of the back room. "Brock! Joy!" She shouted. She tried to reach for a Pokeball from her bag.

"Misty, don't!" Brock shouted. "We'll be okay. Don't do anything stupid." He was pushed out the door by the agent, Joy being lead out directly behind him. Nathan was slung over the shoulder of the second agent, his arms dangling loosely.

The agents dragged Brock, Joy and Nathan to a van stationed just outside the house. Delia and Misty watched with worried silence as the agents got in the van and started to drive away. But before the got to far, a large Pokemon descended to the ground and landed right in front of the van. Its large leathery wings beat, kicking up a cloud of dirt. A large flame burned from the end of its tail.

The headlight shined brightly on the pokemon, A Charizard. The trainer climbed from the back of the pokemon and stepped into the light. A red and white cap perched on his messy black hair. A blue vest rested open to a dark green shirt. A pair of fingerless gloves were worn on his hands. And held in the crook of his arm was a bright yellow Pikachu. Ash Ketchum.

"Hey!" Ash shouted. "What's going on?"

An agent stepped out from the van. "Out of the way kid. We have business to take care of."

"Really? What were you just going at my house?" Ash looked behind the van and saw Misty and his mom still hanging out the doorway. "Mom? Misty? Where's Brock?" Their eyes drifted to the van and then back to Ash. "I see." Ash turned back to the agent. "Let them out."

"Can't do that, kid. The are under arrest for crimes against the Pokemon League." The agent said, in a calm monotone.

"Well, I'm not moving until you let them out." Ash said.

"Very well." The agent pulled a poke ball from his coat. In a blast of white light, a Nidoking appeared. It roared angrily, slamming its fists into the ground. Ash stepped back behind Charizard. "Nidoking, poison sting."

Nidoking opened its mouth and a barrage of poisonous barbs came flying out towards Charizard. "Tail whip!" Ash shouted. Charizard spun around, knocking the barbs away with the flame on its tail. They fell harmlessly to the ground. "Now, Fire Spin!" A blast of flames erupted from Charizard's mouth cycling through the air.

The flames engulfed the Nidoking in a vortex. It whipped its arms and tails, dissipating the flames. Charizard rushed forward and locked its arms around the Nidoking. "Seismic Toss!" Charizard flexed its wings and pushed off into the air, clutching the Nidoking. As it flew, it closed its wings and dropped back down to the ground. Just as it came down, it released the Nidoking, dropping it. It crashed in a puff of dust, Charizard flying off from the attack.

As the dust cleared, the Nidoking lay motionless. Fainted. A beam of red light shot from the agent's Pokeball, recalling the Pokemon. As the first agent stepped back, the second came forward, pulling out his own poke ball. It opened in a flash of light and an Alakazam appeared, it held up its two spoons in an aggressive stance.

Ash withdrew Charizard. He took out another Pokeball and unleashed another Pokemon. A large green and black Pokemon with a long tail that stood on two legs. A Tyranitar. "Tyranitar, Rock Throw!" The dinosaur-like Pokemon reached down to the ground and lifted a rock up. It threw the rock with all its force at the Alakazam.

"Barrier." The agent said. Alakazam's eyes glowed blue and a light aura appeared around it. The rock slammed into the Pokemon, and crumbles instantly. "Psybeam!" A beam of energy shot from the two spoons in Alakazam's hands, striking Tyranitar.

Tyranitar braces itself and digs it feet into the ground. The psychic energy slammed into it, pushing it back. It was pushed back three feet, but as the energy dissipated Tyranitar raised its head angrily. "Hyper Beam!"

Energy gathered in the Pokemon's mouth before being unleashed at the enemy. Alakazam held up its arms for defense, and the Hyper Beam split around it. As it lowered it's arms, it caught sight of Tyranitar charging for it, mouth wide open. "Now use Crunch!" Tyranitar clamped its jaws over Alakazam's body, digging its teeth into the psychic Pokemon. Alakazam cried out and fainted. Tyranitar released its jaws and dropped the Alakazam to the ground. A beam of red light struck the psychic Pokemon and it disappeared into its poke ball.

The agent placed his poke ball away and stepped back. "What is your name, boy?" The agent asked.

"Ash Ketchum."

The other agent quickly ran the name through the onboard computer in the van. He came back out, adjusting his sunglasses. "That name is not in our database. We'll have to take you in for illegal possession of Pokemon without authorization of the Pokemon League." Another set of handcuffs appeared in his hands.

"Yeah, that's not gonna happen." Ash pointed at the agents and Tyranitar advanced. The Pokemon grabbed the two agents and lifted them up, throwing them aside. It walked around to the back of the van and tore the doors away with ease.

Brock's head shot up as the doors were ripped away with the sound of twisting metal. Joy jumped and a small scream escaped her mouth. They stared as the Tyranitar tossed the doors aside. Ash came around the back of the van and peaked inside. "Hey, what's going on?"

"Ash!" Brock jumped to his feet. "I've never been happier to see you." He jumped out the back, Joy right behind him.

Ash set Pikachu down on the bench inside the van and pulled himself inside. He picked up the still comatose Nathan and carried him out. "What did you do to make them come after you?"

"I don't know." Brock said. Ash motioned to Tyranitar. It grabbed the chains of the handcuffs and snapped them. It then did the same to Joy's restraints. "They just showed up and dragged us off. They said something about violating contracts."

"Huh, that's pretty strange." Ash carried Nathan over to Brock and placed the child in his arms. "Well, I think he's gonna be okay. The stuff they gave him should ware off in a few hours." He picked up Pikachu and recalled Tyranitar. "Come on, let's go back inside."


	5. Confrontation

**Confrontation**

The door of Oak's lab creaked open and the Pokemon Professor stepped out. He closed the door behind him and locked it. He didn't know if he would ever be coming back to this place. Not with knowing what he would have to do. He secretly hoped, prayed that somehow Gary had been wrong. That he was mistaken. But he knew that there was no mistake on Gary's part. Why did it have to be him? Oak knew what he would have to do, but he could think of no more dangerous opponent. To bring him down, it would take all his experience and skill. Resting in the pockets of his jacket were Gary's letter and two pokeballs. One contained Gary's Blastiose. The other, Oak's own personal pokemon. He would need both.

Oak stepped out onto the path. The pitch black sky above him dotted with pin pricks of light from each of the stars and the luminiciant light of the full moon. Ahead of him shinned another light. The light of his destination, the Ketchum residence.

As he approached, he saw a black van with its head light on and the back doors flung wide open. Behind it stood four figures. Brock and Joy, Nathan held in his father's arms and his mother tending to him. Along side them was Ash Ketchum, Pikachu cradled in the crook of his arm, and Tyranitar at his side. The large dinosaur-like pokemon turned into a beam of red light as it was recalled into it's pokeball. Ash clipped the capsule device back to his belt. "Come on, let's go inside." Ash started to make his way to the front of the house, where Deliah and Misty stood in waiting.

"So, Ash, when did you get a Tyranitar?" Brock asked.

"Remember the baby Larvitar that we carried with us for a while? Yeah, while in Johto I found it." Ash commented.

Misty raced down from the house and grabbed Ash, throwing her arms around him in a tight embrace. With his free arm, Ash hugged her as well. Pikachu squeaked and squirmed in between them. They held each other for close to 30 seconds before she finally released her hold. "I missed you." A smile ran across Misty's face.

"I missed you, too. I heard about Cerulean."

"I'm sure you did." Oak said, emerging from the shadows and into the porch light of the Ketchum house.

Ash turned to face the Professor. "Hi, Professor Oak. How are you?"

"I've been better. Gary passed away late night." Oak said.

"Oh, God." Ash brought his hand to his face. "That's horrible. What happened?"

"The Gym killer got to him. I don't know why they would go after Gary. But he manged to send me his Blastoise before he the connection cut out." Oak said. He pulled the letter out of his pocket. "Blastoise was holding this. Gary's last words."

Ash's heart began to beat harder in his chest. His pulse raised as Oak unfolded the letter.

"'Gramps,'" Oak began to read, "'I only have a few seconds, so here it is. I love you and I'm sorry I can't say more. I know who the gym killer is." Oak paused for a second and looked up from the letter. "Ash."

All eyes turned on Ash in utter disbelief. Ash stood, stoic and unmoving. Finally his hand slipped off Misty's waist and he walked a little ways away. "So, I've been found out. And now you know."

"Ash, wha..." Misty's voice cracked as she tried to talk, "you're the gym killer?"

Ash waited silently with his back to them, before turning and facing his closest friends and family. After the tense silence, he finally replied, "Yes."

Tears began to well up in Misty's eyes. "Why?" She started to cry. "Why would you do it?"

"Because I've seen there true face. The true intent of the Pokemon League." Ash unshouldered his backpack and pulled out the yellow folder. He tossed it to the ground. "You wanted to know why they were arresting you, Brock? Look in that and see."

Brock, hesitantly, handed Nathan over to Joy and picked up the folder. Opening it up, he saw documents and papers, along with photos of him, Joy and their son. Scanning over the papers, Brock read warrants and charges. "What is all this?"

"They wanted to take you in so that the truth would never be know. Nathan was a loose end. Someone with Joy's DNA. A child of Nurse Joy." Ash said.

"What does that have to do with anything?" Brock asked.

"She is property of the Pokemon League." Ash said.

"People can't be property." Brock retorted.

"But then they don't consider her a person. She is one of many exact genetic replicas created by the Pokemon League. She is a clone. I've seen it. Every time a Nurse Joy or Officer Jenny gets pregnant and she goes in for prenatal care, the fetus is removed and replaced with another clone. It is the way the Pokemon League keeps complete control of the Pokemon centers and police organizations. Why do you think no other Joy's or Jenny's have any other kids?"

"Ash," Brock closed the folder, "You can't honestly believe that."

"Oh, really? Then tell me, when was Nathan conceived?"

"That's a very personal question." Brock retorted.

"During the war." Joy said. "I was helping in the medical shelters and Brock was injured. It was during that time that..."

"And you never made it back for any sort of prenatal work or doctors appointments. So by the time you realized you were pregnant, it was already too late. And now, the Pokemon League is trying to cover it up. They can't have a child of Nurse Joy outside of there control."

"That still doesn't explain why!" Misty shouted. "Why did you do it? The gyms, all their leaders, why did you kill them?"

"Because I learned the truth. I learned it from my father."

A look of fear struck over Deliah's face. Ash had learned that? At the worst possible time.

"After the war, I began my true quest to track down Team Rocket and bring them down. Eventually, I managed to confront Giovanni himself. He told me everything. The Pokemon League, the Gym leaders, the badges, the Tournaments and Championships, all of it a sham. It all exists simply for something like Unova." Ash said. "All the trainers are just soldiers. To be called upon at a moments notice to fight and die for a cause that we don't even know about."

"Ash, that's not true!" Brock shouted.

"You're a part of it too, but it goes much bigger than you. Almost no one knows. Not you, or Misty, not even you, Professor. Only someone as powerful or high ranked as the Elite Four know about it. But Giovanni knew. That's why he created Team Rocket. So that he could work to bring this totalitarianism down. That's why he created Mewtwo, so that he would always have a Pokemon powerful enough to take on and defeat any of the Leagues agents or even the League itself. Only after I defeated him did I learn. And he also told me who I was. And it was this mission in life that made him leave you, Mom."

All eyes turned to Deliah. All in shock. Her hand was held over her mouth and tears streamed down her face. "Ash, I..."

"Should have told me, I know. But I understand why you didn't. In any case, after learning the truth I set about doing what Team Rocket wouldn't. Doing what had to be done. Bringing down the Pokemon League, starting with their gyms. I remember during the war. There was a kid, just got his first pokemon. He was thrown onto the front lines. His starter was no match for anyone. And you know what that war did? It brought out the worst in people. Another trainer attacked the kid with his Scyther. The kid was eviscerated right before my eyes, Brock. I'm not going to let that happen to anyone else."

"By killing more people!" Brock shouted. "Don't you see, Ash? That war brought out the worst in you. You claim to want to stop the Pokemon League's control, but to kill people who have no idea about it?"

Ash shook his head. "I was hoping you'd understand. But I see you are too blind." He turned away and began to walk. "I called you all here so that when I destroyed you gyms you wouldn't be hurt. I'll be on my way. I doubt you'll ever see me again."

Oak pulled one of the poke balls from his jacket and expanded it. "I can't let you leave, Ash. Not now that I know the truth."

Ash stopped in his tracks. "You intend to stop me?"

"It is my duty to bring you to justice." Oak said. He hit the button on the ball and a blast of light emerged, forming into Blastoise once again. It roared and cocked its cannons.

Ash turned to face him, pulling his own Pokeball from his belt. "Very well."


	6. Clash

**Clash**

Ash and Oak stood facing each other. Blastoise stomped the ground, growling at Ash. Ash tossed his poke ball in the air and in a flash of light, Charizard appeared. It flapped its wings and swung its tail, snarling.

"Charizard, Flare Blitz." Ash said. Charizard charged at Blastoise, flames encircling its body. It slammed into the Blastoise, shoving the water Pokémon back.

Blastoise latched hold of Charizard's wings. "Skull Bash!" Oak shouted. Blastoise slammed its head against Charizard's. Charizard roared and stumbled. It shook its head and snarled. It slashed at Blastoise, its claws dragging across the shell.

As Charizard and Blastoise battled, Ash pulled another poke ball, expanding it. It opened with a burst of white light and the hulking green form of Tyranitar appeared. Oak stepped back at the sight of the deadly powerful pokemon.

Ash pointed at Professor Oak. "Thrash."

Tyrannitar roared and charged at Oak. It's mouth agape and teeth bared. Before it could strike, another blast of white light exploded and a huge hulking segmented creature made of rock and metal collided with Tyranitar. The green dinosaur-like pokemon was tossed aside like nothing in the wake of this much larger pokemon.

Steelix lifted the first third of his body up off the ground and stared down at Tyrannitar. Behind it, Brock held an open poke ball out before him. "Brock, stay out of my way." Ash said in a cold stern voice.

"I can't." Brock placed the poke ball back on his belt. "I will not just stand by and let you kill innocents anymore."

"I saved you from the Pokemon League, Brock. I wanted to spare you from the fate the other Gym Leaders suffered. But even after that, you turn against me, too?" Ash asked. "Fine. Tyranitar, use Hyper Beam on Steelix."

Golden energy gathered in Tyranitar's mouth before exploding out in a beam and slamming into the great iron snake. Steelix winced and was pushed back, falling over itself. It wriggled on the ground before righting itself.

"Steelix, Body Slam!" Brock shouted. The iron snake raised it's body off the ground and brought it down with force on Tyranitar. It crashed with enormous force, kicking up a huge cloud of dirt around it. As the dust settled, Brock groaned in frustration. Beneath Steelix, Tyranitar stood firm. The dinosaur pokemon's feet had been pushed eight inches down in the earth and Tyranitar strained under the weight, but it held firm.

"Thrash." Ash commanded. Tyranitar grabbed Steelix and pushed it aside. It slammed the much larger pokemon against the ground, lifted it's head back up only to throw it back down.

"Steelix, break free! Get out of it's grasp!" Steelix struggled and pulled against Tyranitar, but the smaller pokemon kept its hold. Brock turned back to Misty. "Misty, you need to help us."

"What?" She asked.

Ask took another poke ball out and in a flash, Infernape appeared. It raced at Steelix and slammed its flamming fist into the iron snake's face. Steelix growled and crashed to the ground. Tyranitar released its hold in Steelix and turned to the continuing battle between Charizard and Blastoise.

"Misty, please. We can't win without your help."

Misty hesitated for a minute, before gaining her resolve. She pulled off her backpack and pulled it open. Reaching in, she pulled out her own poke ball. Pressing the button, it opened in a flash of white. A serpentine form appeared, crashing into both Tyranitar and Infernape.

gyarados roared in fury. "Hydro-pump!" Misty shouted. A powerful blast of water gushed from the water dragon's mouth and cascaded over the two other pokemon.

"So you turn against me as well?" Ash asked. For the first time, looking truly hurt.

"I'm sorry, Ash. But you're just not the same person I…" Fell in love with. "Once knew."

Ash stared at his shoes for a moment before locking eyes with her. "Fine."

Steelix slowly lifted itself up. The six pokemon faced each other down and the battle began. They fought, grappling, clawing and biting at each other. Steelix swung its tail into Tyranitar. gyarados chomped its jaws at Infernape. Charizard breathed its flames against Blastoise. The Pokemon clashed, reshaping the ground beneath them. After nearly half an hour of fighting, the battle finally came to a close.

"Tyranitar, Hyper Beam." The beam of energy slammed into Steelix and knocked it out. "Infernape, Mega Punch." Delivering a well aimed punch to its face, Infernape brought down gyarados. "Charizard, Seismic Toss." Charizard locked its arms around Blastoise and lifted it up to the sky. Folding its wings, it brought Blastoise back to earth, crashing the giant turtle against the ground. All three pokemon stood triumphant over their fallen adversaries.

Oak, Brock, and Misty each recalled their pokemon. As Oak put Gary's poke ball away, he pulled out his own. "Sorry, Ash. But I'm not done yet." He tossed it in the air and it burst open. A Dragonite, standing over six feet tall, emerged. It flexed its wings and whipped its tail. "Dragonite, extreme speed!"

The dragon pokemon disappeared in a flash of speed and in an instant Infernape was thrown back. I skidded against the ground, coming to a stop at Ash's feet. Already exhausted from battling gyarados, it fainted. Ash recalled it. "Tyranitar, Hyper Beam."

"Dragonite, counter with your own Hyper Beam!" The two pokemon blasted at each other and the mass of energy exploded between them in a blinding flash. As the light began to dim, Dragonite raced forward and grabbed Tyranitar, lifting it up off the ground. Once it got high enough, Dragonite dropped it, sending it plummeting back to the ground.

Charizard took off after Dragonite, the two pokemon clashing in the sky. "Charizard, Overheat!" Ash shouted. Charizard began to turn read and an immense amount of energy erupted from its body. Dragonite crossed its arms over its face as it took the brunt of the attack. Once the heat dissipated, it lowered its arms.

"Now, Dragonite, Extreme Speed!" Oak commanded. Once again in a nearly invisible flash, Dragonite disappeared and reappeared with its horn buried in Charizard's chest. Charizard coughed and stumbled in the sky until it lost control and fell, crashing to the earth.

Ash recalled Charizard as he had done with Tyranitar and Infernape. "You're defeated, Ash."

With cold and unhindered movements, Ash took the last two poke balls off his belt. Both of which were Master Balls. "You've left me with no choice, but to use my final pokemon." They opened and two enormous creatures appeared.

The first was sleek and smooth, with a pure white body and light blue underbelly. It held a long graceful neck up above it and a set of powerful wings folded at its side.

The second was a bird with feathers that shown in seven colors, dazzling even in the night. These two pokemon, of amazing power and legend. Oak had a hard time believing his eyes. These were the two legends of Ecruteak City. The Guardian of the Sea, Lugia; and the Guardian of the Sky, Ho-oh.

Ash walked over to Lugia and climbed up on its back, still cradling the crippled Pikachu in the crook of his arm. The two legends spread their wings, causing gale force winds that buffered everyone around. They took to the air, Ash looking down upon his friends, family, and mentor. "I wanted to spare you, but you've forced my hand!" He shouted down at them. "And now, no one will survive."

Dragonite placed itself between Ash and the professor. "Extreme Speed, Dragonite!" Oak ordered. The dragon vanished as it charged for Lugia.

With calm and demure, Ash spoke. "Steel wing." Ho-oh, moved in front of Ash and it's wings changed from seven colors to a cold gray. It swung them it great power and struck Dragonite, sending the dragon-type cascading to the earth below.

Oak couldn't move. His last pokemon, his most powerful, defeated in a single attack. That must've been the power of these legends. And now, any chance he had to stopping Ash was crushed along with his Dragonite.

"Good-bye." Ash said. "Ho-oh, Sacred Fire."

Ho-oh's beak snapped open and a flame, ablaze in seven colors appeared. As it reared back it's head to attack, the sound of an unusual crackle started to appear in the sky. A black sphere, crackling with purple lightning hurtled down from the sky and slammed into the back of Ho-oh. The great bird screeched and lost control of its fire, which fizzled out.

Ash turned back, but only saw the black expanse of the sky. Suddenly, a blue energy sphere, much larger than the one that struck Ho-oh, slammed into Lugia. The legendary pokemon twisted in the sky, Ash clutching the scales on its back for dear life. As Lugia finally righted itself, Ash saw the face of his attacker. Another pokemon, six feet tall with feline characteristics. A purple body with a thick tail and a set of horn-like ears atop its head. Team Rocket's once secret weapon.

Mewtwo.


	7. Legacy

**Legacy**

Mewtwo hovered in the air directly in front of Ash and Lugia. A tense calm settled between the two, each staring in the other's eyes. Mewtwo's tail whipped slowly from side to side, but aside from that he didn't move.

Staring up from below, Oak, Misty, Brock, Joy and Delia watched with anxious anticipation. "What kind of Pokemon is that?" Oak asked. "I've never heard of any that look like it."

"Mewtwo." Brock said. "A Pokemon created through cloning experiments preformed by Team Rocket. Designed to be the most powerful Pokemon of all, and their ultimate weapon. That is until it chose to leave and live alone. But what's it doing here now?"

Slowly, methodically, Mewtwo lifted one paw out before him and a ball of black energy crackled in his palm. It swung with great force, throwing the Shadow Ball. Lugia reared back and folded its wings over it's face. A sphere of energy surround the Guardian of the Sea and the Shadow Ball dispersed in a cloud of smoke as it hit.

Lugia flared its wings and cried out a loud shrill. It lunged at Mewtwo, snapping its powerful jaws. Mewtwo twisted in the air and dodged. As he flew past Lugia, Mewtwo formed another Shadow Ball and threw it. Too close to dodge of block, Lugia took the full force of the attack and recoiled through the air.

As Lugia struggled to stay airborne, another loud screech split the air. Ho-oh took to the sky, unleashing a huge blast of fire at Mewtwo. A globe of blue energy surrounded the clone Pokemon and dispersed the flames. Once the flames died down, the blue energy field dissipated. But as soon as it did, a beam of golden energy slammed into the clone Pokemon. He cried out in pain and cascaded to the ground.

Lugia and Ho-oh hovered over the fallen Pokemon. Mewtwo lay motionless in the crater it caused. Small at first, but growing stronger, blue electricity sparked along Mewtwo's body until his eyes snapped open and he shot straight up into the air, slamming the full force of his body into Ho-oh. The Legendary Pokemon spiraled through the air until coming to crash near Professor oak's lab.

"Even these two great legends cannot defeat me." He spoke through his psychic powers.

"Why are you here, Mewtwo?" Ash asked.

Mewtwo turned to face the Pokemon trainer sitting atop Lugia. "I am here to put an end to your crusade."

"Why is it of your concern? Didn't you hate humans and how they treated Pokemon? Didn't you want to bring down the league yourself?" Ash asked.

"At one time. I was created to be a tool for Team Rocket, only a weapon. I hated my lot in life, but you helped show me that all life was precious. Life is wonderful, I was told from before I can remember. I learned compassion from you, but in Cerulean city I saw you destroy the Pokemon Gym. Even if the girl wasn't there, how many other people and Pokemon were?" Mewtwo retorted.

"I need to stop the Pokemon League. How many people have they killed? How many young children are thrown out in the wilderness and never make it home to the family waiting for them? How many trainers went to Unova during the war and died? I need to make sure that never happens again."

"By killing more? The Pokemon League is corrupt, but killing people who don't know isn't helping anyone." Mewtwo said. "And now, you're trying to emulate the man that left you and your mother? If you've forgotten, Giovanni was responsible for my creation as well."

"I'm not emulating him!" Ash shouted. "Lugia, Aeroblast!" A golden beam of energy shot from Lugia's mouth. Mewtwo crossed his arms over his face. The blast struck him and send the clone flying back hundreds of feet. When he finally stopped, smoke rose up from the scorched sections of fur on his arms. "That man left my mother when she was in most need. He abandoned us! I'm just doing what he never could. This is my legacy. To end this corruption and bring down the tyranny of the Pokemon League."

"Haven't you abandoned your family as well? Look at them. Each of them were eagerly awaiting your return and wanted to make sure you were alright. But now that you're here it's easy to see that their patience was in vain." Mewtwo said.

"That's unfortunate." Ash replied. "Ho-oh, Sacred Fire!"

Ho-oh, perched up and a stream of flames radiating in seven colors erupted from its beak. Mewtwo had barely enough time to react before being struck. The flames engulfed his body, scorching his fur and sending the cloned Pokemon spiraling towards the earth. He crashed through the roof of the Ketchem house, wood and debris littered around him. Mewtwo twitched and winced as he slowly regained consciousness. His body twisted with pain.

Another sound came to Mewtwo's attention. The sound of a child crying. As he sat up, he noticed a white crib placed in the corner of the room. And within, a baby with a tuff of black hair lay crying. Mewtwo winced as he slowly stood up and walked over to the side of the crib. He gazed down at the child squirming in the crib, unsure of how to feel.

The door to the room burst open and Misty raced in. She shoved Mewtwo aside, briefly stunning the Pokemon, and scooped the child up in her arms. "Shhhh, shhhh, it's okay, Adam." She whispered, tears streaming down her face. "It's okay."

Ash and Lugia flew over the house, prepared to attack. "Aeroblast." Ash commanded. Lugia reared its head back, an orb of golden energy forming in its mouth. The light from this powerful attack shown down on Misty and Mewtwo. Misty clutched the baby against her chest. No time to run. No time to hide. The Aeroblast shot down, obliterating the house.

Debris scattered all over. Smoke rose out from the crater that used to be the Ketchem house. Brock, Joy, Oak, and Delia watched horrified. Unable to fully comprehend what had happened. Silence settled over the group.

Slowly, the smoke began to dissipate. As it did, a blue energy shield emerged. Mewtwo stood next to Misty with his arms stretched over his head, maintaining the shield. Slowly, he lowered his arms and the shield faded. Baby Adam still cried, held tightly in Misty's arms.

Ash heard the child's cries. Looking down on Misty, he saw the baby held in her arms and the wheels began turning in his head. He remembered their one night together. Before he left to confront Team Rocket for the last time. Before he learned the truth about the League. The night they confessed their love and shared it with each other.

Ash pulled a Poke-ball from his belt and recalled Ho-Oh. Once he replaced it, Lugia flapped its powerful wings and took off, soaring into the night sky and disappearing into the darkness.

Misty clutched her baby, watching as the man she used to love flew away. He legs gave out from under her and she folded to the ground; physically, mentally, and emotionally exhausted. She wept.

_5 years later…_

Misty stood outside the gates of Cerulean Elementary School as Adam, just finishing his first day of Kindergarten, ran out to meet her. She scooped him up in her arms and hugged him tight. "Mommy, you're squishing me!" He squeaked.

"I know. You are just so squish able." She set him back down and grabbed hold of his hand. "What happened in school today?"

"We had lunch." He chimed.

"Of course." Misty smiled. "Anything else?"

Adam thought for a second. "Well, I saw some kids' dads. Mommy, where's my dad?"

Misty stopped. She turned away from her son, and then turned back. "He's away. Somewhere." Ash hadn't been seen or heard from since that night. At the same time, Brock and Joy had gone into hiding, disappearing with their son. Mewtwo didn't stay around long after Ash left. He also flew away never to be seen again. Misty shook her head and returned to reality. "Come on, let's go get some ice cream."


	8. Author's Note

**Author's Note:**

This story came about from a discussion between myself and a friend about the underlying darkness of the Pokemon universe. And more than just the animal fighting and potential child abuse going on. More of the reasons for said child abuse and animal fighting. A question of, what kind of culture would send 10 year old kids into the wilderness with only a deadly powerful creature to act as protection and means of survival? Why does every Nurse Joy and Officer Jenny look exactly the same? Why is the society based around collecting badges and training these deadly powerful earth shattering monsters to fight?

And then things started to fall into place. In a world of fire-breathing dragons, giant water serpents, and lightning shooting mice, there would be no need for other types of weapons like guns and tanks and missiles. The Pokemon are the weapons of war. And the trainers are the soldiers.

This story was meant to be a sort of Pokemon version of Watchmen, and at the beginning that's easy to see. Someone killing off Gym Leaders, the same as someone killing of costumed heroes. Now, this story is not as good as Watchmen, but I figured it would never truly be. Many of the darker aspects of Pokemon that I brought up in this story were indeed addressed in Generation 5 of the main games. However, when I started writing this story, I hadn't played any of those games yet. If I had, the two legendary Pokemon Ash had would've been Zekrom and Rashirim rather than Lugia and Ho-Oh.

Mewtwo's inclusion in the story can be summed up as a reversal from the first time he and Ash met. Mewtwo used to be angry at the world and at humans, wanting to prove his worth, that despite being a clone he was still worth something. Ash's sacrifice in the first movie showed him that all life was precious. And now, after everything Ash has seen and having everything he knew shattered, Mewtwo had to appear and try to teach Ash the very thing Ash had taught him.

As for the ending, it was left like that for a reason. What truly was Ash's legacy to the world? Even after all the pain and suffering he caused, the Pokemon league was not brought down. And the damage he brought to them, can be repaired. In the end of everything he tried, nothing really changed. He only succeeded in ruining the lives of everyone close to him. Again, bringing the Watchmen parallel back. Ozymendias's plan didn't necessarily bring an end to war, and neither did Ash's plan.

If you feel you want to expand of this idea and this take on the Pokemon universe, be my guest. But for me, this is the end of this chapter to that story.


End file.
